#!/usr/bin/env python
 
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from corebio import *
from corebio.seq import *
from corebio.seq_io import *
from test_corebio import *
from corebio.seq_io import phylip_io

from corebio._py3k import StringIO

import unittest

class test_phylip_io(unittest.TestCase) :

    def test_read(self) :
        f = testdata_stream("phylip_test_1.phy")
        seqs = phylip_io.read(f)
        #print seqs
        self.assertEqual(len(seqs), 10)
        self.assertEqual(seqs[0].name, "Cow")
        self.assertEqual(len(seqs[1]), 234)
        f.close()
    
    def test_parse_plain_fail(self) :
        # should fail with parse error
        f = StringIO(plain_io.example)
        self.assertRaises(ValueError, 
            phylip_io.read, f  )
    
    def test_parse_phylip_test_2(self):
        f = testdata_stream('phylip_test_2.phy')
        seqs = phylip_io.read(f)
        self.assertEqual(len(seqs), 6)
        self.assertEqual(len(seqs[0]), 20)
        self.assertEqual(str(seqs[1]), "CGTTACTCGTTGTCGTTACT")
        self.assertEqual(seqs[1].name, "Hesperorni")
        f.close()
    
    def test_parse_clustal_fail(self) :
        # should fail with parse error
        f = StringIO(clustal_io.example)
        self.assertRaises(ValueError, 
            phylip_io.read, f , protein_alphabet )
    
    def test_parse_phylip_test_3(self):
        f = testdata_stream('phylip_test_3.phy')
        seqs = phylip_io.read(f)
        self.assertEqual(len(seqs), 6)
        self.assertEqual(len(seqs[0]), 20)
        self.assertEqual(str(seqs[1]), "CGTTACTCGTTGTCGTTACT")
        self.assertEqual(seqs[1].name, "Hesperorni")
        f.close()
    
    def test_parse_phylip_test_4(self):
        f = testdata_stream('phylip_test_4.phy')
        seqs = phylip_io.read(f)
        self.assertEqual(len(seqs), 6)
        self.assertEqual(len(seqs[0]), 25)
        self.assertEqual(str(seqs[1]), "GTGGTGGTGGGCGCCGGCCGTGTGG")
        self.assertEqual(seqs[2].name, "ddrasa")
        f.close()
    
    
    def test_parse_phylip_test_5(self):
        f = testdata_stream('phylip_test_5.phy')
        seqs = phylip_io.read(f)
        self.assertEqual(len(seqs), 6)
        self.assertEqual(len(seqs[0]), 50)
        self.assertEqual(str(seqs[1]), "GTGGTGGTGGGCGCCGGCCGTGTGGGTGGTGGTGGGCGCCGGCCGTGTGG")
        self.assertEqual(seqs[2].name, "ddrasa")
        f.close()
        
    def test_parse_wrong_phylip_codes_1(self):
        f = testdata_stream('phylip_test_6.corrupt.phy')
        self.assertRaises(ValueError, 
            phylip_io.read, f , protein_alphabet )
        f.close()
        
    def test_parse_wrong_phylip_codes_2(self):
        f = testdata_stream('phylip_test_7.corrupt.phy')
        self.assertRaises(ValueError, 
            phylip_io.read, f , protein_alphabet )
        f.close()

    def test_parse_phylip_dna(self):
        f = testdata_stream('dna.phy')
        seqs = phylip_io.read(f)
        self.assertEqual(len(seqs), 10)
        self.assertEqual(len(seqs[0]), 705)
        self.assertEqual( str(seqs[1][0:10]), "ATGGCACACC")
        self.assertEqual(seqs[2].name, "Chicken")
        f.close()
   
             
if __name__ == '__main__':
    unittest.main()
